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Jul 23, 2019

Extracting fsspec from Dask

By

TL;DR

fsspec, the new base for file system operations in Dask, Intake, s3fs, gcsfs and others,is now available as a stand-alone interface and central place to develop new backendsand file operations. Although it was developed as part of Dask, you no longer need Daskto use this functionality.

Introduction

Over the past few years, Dask’s IO capability has grown gradually and organically, toinclude a number of file-formats, and the ability to access data seamlessly on variousremote/cloud data systems. This has been achieved through a number of sister packagesfor viewing cloud resources as file systems, and dedicated code in dask.bytes.Some of the storage backends, particularly s3fs, became immediately useful outside ofDask too, and were picked up as optional dependencies by pandas, xarray and others.

For the sake of consolidating the behaviours of thevarious backends, providing a single reference specification for any new backends,and to make this set of file system operations available even without Dask, Icreated fsspec.This last week, Dask changed to use fsspec directly for itsIO needs, and I would like to describe in detail here the benefits of this change.

Although this was done initially to easy the maintenance burden, the important takeawayis that we want to make file systems operations easily available to the whole pydata ecosystem,with or without Dask.

History

The first file system I wrote was hdfs3, a thin wrapperaround the libhdfs3 C library. At the time, Dask had acquired the ability to run on adistributed cluster, and HDFS was the most popular storage solution for these (in thecommercial world, at least), so a solution was required. The python API closely matchedthe C one, which in turn followed the Java API and posix standards. Fortunately, python alreadyhas a file-like standard, soproviding objects that implemented that was enough to make remote bytes available to manypackages.

Pretty soon, it became apparent that cloud resources would be at least as important as in-clusterfile systems, and so followed s3fs,adlfs, and gcsfs.Each followed the same pattern, but with some specific code for the given interface, andimprovements based on the experience of the previous interfaces. During this time, Dask’sneeds also evolved, due to more complex file formats such as parquet. Code to interface tothe different backends and adapt their methods ended up in the Dask repository.

In the meantime, other file system interfaces arrived, particularlypyarrow’s, which had its own HDFSimplementation and direct parquet reading. But we would like all of the tools inthe ecosystem to work together well, so that Dask can read parquet using eitherengine from any of the storage backends.

Code duplication

Copying an interface, adapting it and releasing it, as I did with each iteration of the file system,is certainly a quick way to get a job done. However, when you then want to change the behaviour, oradd new functionality, it turns out you need to repeat the work in each place(violating the DRY principle) or havethe interfaces diverge slowly. Good examples of this were glob and walk, which supported variousoptions for the former, and returned different things (list, versions dir/files iterator) for thelatter.

>>> fs = dask.bytes.local.LocalFileSystem()
>>> fs.walk('/home/path/')
<iterator of tuples>


>>> fs = s3fs.S3FileSystme()
>>> fs.walk('bucket/path')
[list of filenames]

We found that, for Dask’s needs, we needed to build small wrapperclasses to ensure compatible APIs to all backends, as well as a class for operating on the localfile system with the same interface, and finally a registry for all of these with various helperfunctions. Very little of this was specific to Dask, with only a couple offunctions concerning themselves with building graphs and deferred execution. It did, however,raise the important issue that file systems should be serializable and that there shouldbe a way to specify a file to be opened, which is also serializable (and ideally supportstransparent text and compression).

New file systems

I already mentioned the effort to make a local file system class which met the same interface asthe other ones which already existed. But there are more options that Dask users (and others)might want, such as ssh, ftp, http, in-memory, and so on. Following requests from users to handle these options,we started to write more file system interfaces, which all lived within dask.bytes; but it was unclearwhether they should only support very minimal functionality, just enough to get something done fromDask, or a full set of file operations.

The in-memory file system, in particular, existed in an extremely long-lived PR - it’s notclear how useful such a thing is to Dask, when each worker has it’s own memory, and so seesa different state of the “file system”.

Consolidation

file system Spec, later fsspec, was born out of a desireto codify and consolidate the behaviours of the storage backends, reduce duplication, and provide thesame functionality to all backends. In the process, it became much easier to write new implementationclasses: see the implementation,which include interesting and highly experimental options such as the CachingFileSystem, whichmakes local copies of every remote read, for faster access the second time around. However, moreimportant main-stream implementations also took shape, such as FTP, SSH, Memory and webHDFS(the latter being the best bet for accessing HDFS from outside the cluster, following all theproblems building and authenticating with hdfs3).

Furthermore, the new repository gave the opportunity to implement new features, which would then havefurther-reaching applicability than if they had been done in just selected repositories. Examples includeFUSE mounting, dictionary-style key-value views on file systems(such as used by zarr), and transactional writing offiles. All file systems are serializable and pyarrow-compliant.

Usefulness

Eventually it dawned on my that the operations offered by the file system classes are very usefulfor people not using Dask too. Indeed, s3fs, for example, sees plenty of use stand-alone, or inconjunction with something like fastparquet, which can accept file system functions to its method,or pandas.

So it seemed to make sense to have a particular repo to write out the spec that a Dask-compliantfile system should adhere to, and I found that I could factor out a lot of common behaviour fromthe existing implementations, provide functionality that had existed in only some to all, andgenerally improve every implementation along the way.

However, it was when considering fsspec in conjunction with Intakethat I realised how generally useful a stand-alone file system package can be: the PRimplemented a generalised file selector that can browse files in any file system that wehave available, even being able, for instance, to view a remote zip-file on S3 as abrowseable file system. Note that, similar to the general thrust of this blog, thefile selector itself need not live in the Intake repo and will eventually become eitherits own thing, or an optional feature of fsspec. You shouldn’t need Intake either justto get generalised file system operations.

Final Thoughts

This work is not quite on the level of “protocol standards” such as the well-know python bufferprotocol, but I think it is a useful step in making data in various storage services availableto people, since you can operate on each with the same API, expect the same behaviour, andcreate real python file-like objects to pass to other functions. Having a single central repolike this offers an obvious place to discuss and amend the spec, and build extra functionalityonto it.

Many improvements remain to be done, such as support for globstrings in more functions, ora single file system which can dispatch to the various backends depending on the form of theURL provided; but there is now an obvious place for all of this to happen.